Precipitation of nucleic acids is a common procedure in molecular biology research. Precipitation is often necessary to concentrate dilute solutions of a nucleic acid or to change the solvent in which the nucleic acid is dissolved. In practice, a salt is added to the nucleic acid solution followed by a suitable amount of an alcohol such as ethanol or isopropanol. The sample is incubated at a suitable temperature until nucleic acid molecules precipitate. The nucleic acid is then harvested by centrifugation.
When working with dilute nucleic acid solutions (≦10 μg/ml) or small amounts of DNA or RNA (≦1 μg), it is often desirable to increase the precipitation efficiency by including a carrier molecule. In addition, carriers can increase the precipitation rate and can reduce the overall time necessary to recover a nucleic acid from solution. A carrier molecule can increase the amount of material recovered from dilute solutions or increase recovery of small amounts of nucleic acids.
Wallace, D. M., (1987) Meth. Enzymol. 152, 41-48 reviewed the requirements and strategies used to precipitate nucleic acids. Wallace is incorporated herein by reference as background to the present invention. Wallace reports the use of carrier molecules such as transfer RNA (tRNA) and purified glycogen to increase the nucleic acid precipitation rate and efficiency.
Glycogen is a high molecular weight polysaccharide composed of repeating units of D-glucopyranose residues joined by (1→4)-α-D-glucosidic linkages with branch points at position C-6 at one out of 12 residues on average. The branch lengths are in the range of 4-8 residues (Bahl, O. P. and Smith, F. J., (1966) Org. Chem., 31, 2915-2920). The base structure (excluding branch structures) is:

Glycogen is recognized to be a good carrier in nucleic acid precipitation methods because it shares solubility and precipitation characteristics with nucleic acids. Since a nucleic acid backbone is also composed of repeating units, namely ribose or deoxyribose connected via phosphodiester linkages, both nucleic acids and glycogen are soluble in aqueous solutions and precipitate (aggregate) when the dielectric constant is lowered by the added alcohol. Glycogen is also advantageously used as a carrier because it is charge-neutral and causes no inhibition of common enzymatic reactions performed with nucleic acids (e.g.: restriction digestion, cDNA synthesis, transcription, ligation, amplification, sequencing, tailing, etc.). For some applications, glycogen is preferred over tRNA, which can interfere with some enzymatic reactions such end-labeling with kinase.
Despite the wide-ranging use of nucleic acid precipitation in almost all common molecular biology methods, the technique is often prone to unpredictable failure. Even when a carrier molecule is included to increase the total amount of precipitated nucleic acid, nucleic acid pellets are easily lost during the removal of supernatant phases, particularly when working with small amounts (<10 μg) of nucleic acids, or when using carriers, which are not readily visible to the unaided eye. In addition, protocols often require that nucleic acid pellets be washed with alcohol solutions and dried under vacuum prior to re-solubilization in aqueous buffers. These steps often result in the dislodging of pelleted nucleic acids which are easily lost during subsequent handling.
It would be desirable to be able to monitor the presence and location of nucleic acid during a precipitation method to prevent inadvertent loss of pelleted material.